The store was pelted with eggs and a manager was assaulted when employees refused to open the store, the Los Angeles Times reported. Many of the people in line, including some who had brought sleeping bags and camped out overnight, were believed to be scalpers, the newspaper said.
Apple spokeswoman Carolyn Wu said the store was prevented from opening because of the crowd.
"To ensure the safety of our customers and employees, [the] iPhone will not be available in our retail stores in Beijing and Shanghai for the time being," Wu said.
The Times said the iPhone is still available online through its service provider, China Unicom, to customers who commit to multiyear contracts.
Apple's five official stores in Shanghai and Beijing generate more revenue on average than any other Apple stores in the world, the California-based company said last year. Sales in China rose to $13 billion from $3 billion for the fiscal year ended Sept. 24, Apple said.